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At least 793 records · Page 44

Analysis of Potential Leakage Pathways and Mineralization within Caprocks for Geologic Storage of CO 2

We used a multifaceted approach to investigate the nature of caprocks above, and the interface between, reservoir-quality rocks that might serve as targets for carbon storage. Fieldwork in southeastern Utah examined the regional- to m-scale nature of faults and fractures across the sedimentiological interfaces. We also used microscopic analyses and mechanical modeling to examine the question as to how the contacts between units interact, and how fractures may allow fluids to move from reservoirs to caprock. Regional-­scale analyses using ASTER data enabled us to identify location of alteration, which led to site-­specific studies of deformation and fluid flow. In the Jurassic Carmel Formation, a seal for the Navajo Sandstone, we evaluated mesoscale variability in fracture density and morphology and variability in elastic moduli in the Jurassic Carmel Formation, a proposed seal to the underlying Navajo Sandstone for CO 2 geosequestration. By combining mechano-stratigraphic outcrop observations with elastic moduli derived from wireline log data, we characterize the variability in fracture pattern and morphology with the observed variability in rock strength within this heterolithic top seal. Outcrop inventories of discontinuities show fracture densities decrease as bed thickness increases and fracture propagation morphology across lithologic interfaces vary with changing interface type. Dynamic elastic moduli, calculated from wireline log data, show that Young’s modulus varies by up to 40 GPa across depositional interfaces, and by an average of 3 GPa across the reservoir/seal interface. We expect that the mesoscale changes in rock strength will affect the distributions of localized stress and thereby influence fracture propagation and fluid flow behavior within the seal. These data provide a means to closely tie outcrop observations to those derived from subsurface data and estimates of subsurface rock strength. We also studied damage zones associated normal faults in the Permian Cedar Mesa Sandstone, southeastern Utah. These faults are characterized by a single slip surfaces and damage zones containing deformation bands, veins, and joints. Field observations include crosscutting relationships, permeability increase, rock strength decrease, and ultraviolet light induced mineral fluorescence within the damage zone. These field observations combined with the interpreted paragenetic sequence from petrographic analysis, suggests a deformation history of reactivation and several mineralization events in an otherwise low-permeability fault. All deformation bands and veins fluoresce under ultraviolet light, suggesting connectivity and a shared mineralization history. Pre-­existing deformation features act as loci for younger deformation and mineralization events, this fault and its damage zone illustrate the importance of the fault damage zone to subsurface fluid flow. We model a simplified stress history in order to understand the importance of rock properties and magnitude of tectonic stress on the deformation features within the damage zone. The moderate confining pressures, possible variations in pore pressure, and the porous, fine-­grained nature of the Cedar Mesa Sandstone results in a fault damage zone characterized by enhanced permeability, subsurface fluid flow, and mineralization. Structural setting greatly influences fracture spacing and orientation. Three structural settings were examined and include fault proximity, a fold limb of constant dip, and a setting proximal to the syncline hinge. Fracture spacing and dominant fracture orientation vary at each setting and distinctions between regional and local paleo-stress directions can be made. Joints on the fold limb strike normal to the fold axis/bedding and are interpreted to be sub-parallel to the maximum regional paleo-stress direction as there is no fold related strain. Joints proximal to faults and the syncline hinge may have formed under local stress conditions associated with folding and faulting, and in some cases, are perpendicular to the maximum regional paleo-stress direction. Macroscale analyses of the Iron Wash fault, which cuts most of the stratigraphy of the reservoir- seal analogs, reveals that seal bypass occurs along faults with mixed lithologic composition. While portions of the fault may be effective seals, when modeled as a whole the fault zone cannot support a high CO 2 column. We adapted oil-field methods to calculate column heights and sealing capacities. Examination of the burial and tectonic histories of the rocks, coupled with field- and micro-­scale studies, allow us to examine the potential for seal failure using basic rock mechanics failure analyses. These studies reveal that the sealing lithologies experienced multiple episodes of deformation that resulted in numerous fractures and small faults. In a stress state based on burial history and overburden loads, we show that most of the seals could fail with normal to slightly excess pore pressures.

58 GEOSCIENCES↗

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

Emerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗

Optimization models for integrated biorefinery operations

Variations of physical and chemical characteristics of biomass lead to an uneven flow of biomass in a biorefinery, which reduces equipment utilization and increases operational costs. Uncertainty of biomass supply and high processing costs increase the risk of investing in the US’s cellulosic biofuel industry. We propose a stochastic programming model to streamline processes within a biorefinery. A chance constraint models system’s reliability requirement that the reactor is operating at a high utilization rate given uncertain biomass moisture content, particle size distribution, and equipment failure. The model identifies operating conditions of equipment and inventory level to maintain a continuous flow of biomass to the reactor. Furthermore, the sample average approximation method approximates the chance constraint and a bisection search-based heuristic solves this approximation. A case study is developed using real-life data collected at Idaho National Laboratory’s biomass processing facility. An extensive computational analysis indicates that sequencing of biomass bales based on moisture level, increasing storage capacity, and managing particle size distribution, increases utilization of the reactor and reduces operational costs.

09 BIOMASS FUELS↗

Identification and functional characterization of three type III polyketide synthases from Aquilaria sinensis calli

Type III polyketide synthases (PKSs) play an important role in biosynthesis of various plant secondary metabolites and plant adaptation to environmental stresses. Aquilaria sinensis (A. sinensis) is the main plant species for production of agarwood, little is known about its PKS family. In this study, AsCHS1 and two new type III PKSs, AsPKS1 and AsPKS2, were isolated and characterized in A. sinensis calli. The comparative sequence and phylogenetic analysis indicated that AsPKS1 and AsPKS2 belonged to non-CHS group different from AsCHS1. The recombinant AsPKS1 and AsPKS2 produced the lactone-type products, suggesting their different enzyme activities from AsCHS1. Three PKS genes had a tissues-specific pattern in A. sinensis. Moreover, we examined the expression profiles of three PKS genes in calli under different abiotic stresses and hormone treatments. AsCHS1 transcript was most significantly induced by salt stress, AsPKS1 abundance was most remarkably enhanced by CdCl{sub 2} treatment, while AsPKS2 expression was most significantly induced by mannitol treatment. Furthermore, AsCHS1, AsPKS1 and AsPKS2 expression was enhanced upon gibberellins (GA3), methyl jasmonate (MeJA), or salicylic acid (SA) treatment, while three PKS genes displayed low transcript levels at the early stage under abscisic acid (ABA) treatment. In addition, three GFP:PKSs fusion proteins were localized in the cytoplasm and cell wall in Nicotiana benthamiana cells. These results indicated the multifunctional role of three type III PKSs in polyketide biosynthesis, plant resistance to abiotic stresses and signal transduction. - Highlights: • Two new PKS genes (AsPKS1 and AsPKS2) were isolated and characterized from A. sinensis. • The recombinant AsPKS1 and AsPKS2 catalyzed lactone-type products in vitro. • AsCHS1, AsPKS1 and AsPKS2 were involved in plant responses to abiotic stresses and hormone stimuli. • Our results also indicated that AsCHS1, AsPKS1 and AsPKS2 were predominantly localized in the cytoplasm and cell wall.

60 APPLIED LIFE SCIENCES↗

Homology modeling and docking of AahII-Nanobody complexes reveal the epitope binding site on AahII scorpion toxin

Highlights: • AahII specific nanobodies share common CDRs sequence patterns. • Residues forming sequences' pattern interact specifically with AahII. • CDR1 Tyr27, Tyr29 and Ser30 polar residues are involved in AahII neutralization. • Interacting AahII Arg62/NbAahII10 CDR3 Asp112 charged residues are crucial. • AahII-NbAahII10 trapping involves a distinct toxin 3D orientation. Scorpion envenoming and its treatment is a public health problem in many parts of the world due to highly toxic venom polypeptides diffusing rapidly within the body of severely envenomed victims. Recently, 38 AahII-specific Nanobody sequences (Nbs) were retrieved from which the performance of NbAahII10 nanobody candidate, to neutralize the most poisonous venom compound namely AahII acting on sodium channels, was established. Herein, structural computational approach is conducted to elucidate the Nb-AahII interactions that support the biological characteristics, using Nb multiple sequence alignment (MSA) followed by modeling and molecular docking investigations (RosettaAntibody, ZDOCK software tools). Sequence and structural analysis showed two dissimilar residues of NbAahII10 CDR1 (Tyr27 and Tyr29) and an inserted polar residue Ser30 that appear to play an important role. Indeed, CDR3 region of NbAahII10 is characterized by a specific Met104 and two negatively charged residues Asp115 and Asp117. Complex dockings reveal that NbAahII17 and NbAahII38 share one common binding site on the surface of the AahII toxin divergent from the NbAahII10 one's. At least, a couple of NbAahII10 – AahII residue interactions (Gln38 – Asn44 and Arg62, His64, respectively) are mainly involved in the toxic AahII binding site. Altogether, this study gives valuable insights in the design and development of next generation of antivenom.

60 APPLIED LIFE SCIENCES↗

Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomics provides insights into the cold adaptation of endophytic fungi associated with Deschampsia antarctica

Endophytic fungi from Deschampsia antarctica , the southernmost flowering plant, provide insights into the cold adaptation mechanisms of plant-associated fungi in extreme environments. This study presents the genome sequences and comparative analysis of eight fungal isolates from D. antarctica leaves. These Antarctic fungal isolates were analyzed alongside 121 plant-associated fungal genomes to uncover signatures of adaptation and endophytic specialization. Antarctic endophytes show striking patterns, including reduced genome size (∼26.3 Mb on average), streamlined gene content (∼8844 genes), and notably small secretomes (∼288 proteins). Despite this reduced gene repertoire, they maintain a robust set of genes encoding carbohydrate-active enzymes (CAZymes) but lack those for lignin and bacterial cell wall degradation, indicating a symbiotic lifestyle that avoids host damage and predation. One isolate, Alternaria sp. UNIPAMPA017 stood out, with 26% of its genome occupied by transposable elements. Lifestyle, rather than phylogeny, was the main driver of CAZyme and secretome profiles, underscoring ecological convergence. Compared to endophytes from Arabidopsis and Populus, D. antarctica endophytes harbor fewer pectin-degrading enzymes, reflecting their adaptation to the cell wall structure of their monocot host. Together, these fungi reveal a pattern of genomic reduction and functional fine-tuning, hallmarks of life adapted to persist in cold, nutrient-scarce niches.

Ascomycota↗

Initial precipitation and hardening mechanism during non-isothermal aging in an Al–Mg–Si–Cu 6005A alloy

The characterization of precipitation and hardening mechanism during non-isothermal aging had been investigated using high resolution transmission electron microscopy for an Al–Mg–Si–Cu 6005A alloy. It was proposed that the needle-shaped β″ precipitates with a three-dimension coherency strain-field and an increased number density in the Al matrix provided the maximum strengthening effect for the Al–Mg–Si–Cu 6005A alloy. Simultaneously, it was also found that the formation and evolution of clusters in the early precipitation were associated with the vacancy binding energy, during which Si atoms played an important role in controlling the numbers density of Mg/Si co-clusters, and the excess Si atoms provided the increased number of nucleation sites for the subsequent precipitates to strengthen and improve the precipitation rate. Finally, based on the experimental observation and theoretical analysis, the precipitation sequence during the early precipitation in the Al–Mg–Si–Cu 6005A alloy was proposed as: supersaturated solid solution → Si-vacancy pairs, Mg-vacancy pairs and Mg clusters → Si clusters, and dissolution of Mg clusters → Mg atoms diffusion into the existing Si clusters → Mg/Si co-clusters → GP zone. - Highlights: • β″ precipitates provide the maximum strengthening effect for the 6005A alloy. • Si atoms play an important role in controlling the numbers of Mg/Si co-clusters. • The early aging sequence is deduced based on the solute-vacancy binding energy.

36 MATERIALS SCIENCE↗

Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis , for production of citramalate

Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate pro- duction. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.

59 BASIC BIOLOGICAL SCIENCES↗

A novel pathogenic aviadenovirus from red-bellied parrots (Poicephalus rufiventris) unveils deep recombination events among avian host lineages

Competing roles of coevolution, selective pressure and recombination are an emerging interest in virus evolution. We report a novel aviadenovirus from captive red-bellied parrots (Poicephalus rufiventris) that uncovers evidence of deep recombination among aviadenoviruses. The sequence identity of the virus was most closely related to Turkey adenovirus D (42% similarity) and other adenoviruses in chickens, turkeys and pigeons. Sequencing and comparative analysis showed that the genome comprised 40,930 nucleotides containing 42 predicted open reading frames (ORFs) 19 of which had strong similarity with genes from other adenovirus species. The new genome unveiled a lineage that likely participated in deep recombination events across the genus Aviadenovirus accounting for an ancient evolutionary relationship. We hypothesize frequent host switch events and recombination among adenovirus progenitors in Galloanserae hosts caused the radiation of extant aviadenoviruses and the newly assembled Poicephalus adenovirus genome points to a potentially broader host range of these viruses among birds. - Highlights: •Shows how a single new genome can change overall phylogeny. •Reveals host switch events among adenovirus progenitors in Galloanserae hosts. •Points to a potentially broader host range of adenoviruses among birds and wildlife .

60 APPLIED LIFE SCIENCES↗

Predicting Anaerobic Membrane Bioreactor Performance Using Flow-Cytometry-Derived High and Low Nucleic Acid Content Cells

Having a tool to monitor the microbial abundances rapidly and to utilize the data to predict the reactor performance would facilitate the operation of an anaerobic membrane bioreactor (AnMBR). This study aims to achieve the aforementioned scenario by developing a linear regression model that incorporates a time-lagging mode. The model uses low nucleic acid (LNA) cell numbers and the ratio of high nucleic acid (HNA) to LNA cells as an input data set. First, the model was trained using data sets obtained from a 35 L pilot-scale AnMBR. The model was able to predict the chemical oxygen demand (COD) removal efficiency and methane production 3.5 days in advance. Subsequent validation of the model using flow cytometry (FCM)-derived data (at time t – 3.5 days) obtained from another biologically independent reactor did not exhibit any substantial difference between predicted and actual measurements of reactor performance at time t. Further cell sorting, 16S rRNA gene sequencing, and correlation analysis partly attributed this accurate prediction to HNA genera (e.g., Anaerovibrio and unclassified Bacteroidales) and LNA genera (e.g., Achromobacter, Ochrobactrum, and unclassified Anaerolineae). In summary, our findings suggest that HNA and LNA cell routine enumeration, along with the trained model, can derive a fast approach to predict the AnMBR performance.

42 ENGINEERING↗

Chemically Recyclable Analogs of Styrene–Butadiene Copolymers Enabling Perfectly Linear Ethylene–Styrene Materials with Random Phenyl Distribution

Copolymerization of cyclopentene (CP) and 4-phenylcyclopentene (4PCP) at a full range of comonomer feed ratios is reported using Ru-based ring-opening metathesis polymerization (ROMP) yielding homogeneous copolymers analogous to poly(styrene-ran-1,4-butadiene) and poly(ethylene-ran-styrene) copolymers following hydrogenation under mild conditions. In all cases, total monomer conversions of 86%–92% yielded copolymers with compositions within 4% of monomer feeds. Analysis of equilibrium copolymerization thermodynamics, rarely performed on two cycloolefin monomers with low ring strain energies, provides rational design strategies for negotiating two monomers with different equilibrium monomer concentrations. Inverse-gated decoupled 13 C NMR analysis of dyad sequences on the resulting copolymer microstructures concludes a near-random distribution of comonomer units. The copolymers produced from ROMP have number-average molar masses up to 60 kg mol –1 , moderate dispersities (1.5 ± 0.1), and high trans olefin content (86% ± 2%) while glass-transitions temperatures follow the Fox equation and span the full range between homopolymer extremities of PCP (−96 °C) and P4PCP (17 °C). Unlike most prevulcanized elastomers, these materials undergo facile chemical recycling to monomer, producing complete ring-closing metathesis depolymerization (RCMD) of the polymer back to the CP comonomers. Quantitative olefin hydrogenation produced perfectly linear polyethylene with 4%–16% of the backbone carbons containing a phenyl pendant, analogous to ES copolymers with up to 71.5% w/w styrene units but with random distribution of the aromatic pendants. Thermal properties of these materials are discussed, which span from semicrystalline to amorphous, and with T g values notably less than the reported ES copolymer analogs at similar compositions.

animal feed↗

Collaborative cloud-enabled tools allow rapid, reproducible biological insights

Microbial ecologists today face critical computational barriers. The rapid increase in the quantity of data acquired by modern sequencing instruments makes analysis by hand infeasible, and even software developed just a few years ago cannot scale to modern data sets. As a result, making advanced, scalable algorithms and large-scale computational resources available to end-users is necessary to advancing our understanding of microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

Sparse panicle1 is required for inflorescence development in Setaria viridis and maize

Setaria viridis is a rapid-life-cycle model panicoid grass. Here, to identify genes that may contribute to inflorescence architecture and thus have the potential to influence grain yield in related crops such as maize, we conducted an N-nitroso-N-methylurea (NMU) mutagenesis of S. viridis and screened for visible inflorescence mutant phenotypes. Of the approximately 2,700 M 2 families screened, we identified four recessive sparse panicle mutants (spp1-spp4) characterized by reduced and uneven branching of the inflorescence. To identify the gene underlying the sparse panicle1 (spp1) phenotype, we performed bulked segregant analysis and deep sequencing to fine map it to an approximately 1 Mb interval. Within this interval, we identified disruptive mutations in two genes. Complementation tests between spp1 and spp3 revealed they were allelic, and deep sequencing of spp3 identified an independent disruptive mutation in SvAUX1 (AUXIN1), one of the two genes in the ~1 Mb interval and the only gene disruption shared between spp1 and spp3. SvAUX1 was found to affect both inflorescence development and root gravitropism in S. viridis. A search for orthologous mutant alleles in maize confirmed a very similar role of ZmAUX1 in maize, which highlights the utility of S. viridis in accelerating functional genomic studies in maize.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of $\mathrm{IOMA}$-class neutralizing antibodies targeting the $\mathrm{CD4}$-binding site on the $\mathrm{HIV}$-1 envelope glycoprotein

A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.

59 BASIC BIOLOGICAL SCIENCES↗

Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida

Abstract The genome-scale model of metabolism and gene expression (ME-model) forPseudomonas putidaKT2440,iPpu1676-ME, provides a comprehensive representation of biosynthetic costs and proteome allocation. Compared to a metabolic-only model,iPpu1676-ME significantly expands on gene expression, macromolecular assembly, and cofactor utilization, enabling accurate growth predictions without additional constraints. Multi-omics analysis using RNA sequencing and ribosomal profiling data revealed translational prioritization inP. putida, with core pathways, such as nicotinamide biosynthesis and queuosine metabolism, exhibiting higher translational efficiency, while secondary pathways displayed lower priority. Notably, the ME-model significantly outperformed the M-model in alignment with multi-omics data, thereby validating its predictive capacity. Thus,iPpu1676-ME offers valuable insights intoP. putida’s proteome allocation and presents a powerful tool for understanding resource allocation in this industrially relevant microorganism.

Mathematical & Computational Biology↗

Plant single-cell solutions for energy and the environment

Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species’ cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.

59 BASIC BIOLOGICAL SCIENCES↗